Two goals from Yaya Touré and Mario Balotelli's penalty on the stroke of half-time sealed the victory and took City two points ahead of SSC Napoli, meaning they will qualify with a win in Italy on 22 November. But despite the result leaving Villarreal eliminated without a point thus far the home side showed pride and spirit to limit the damage given their debilitating circumstances.

Initially it was hard to gauge that the Yellow Submarine has been shipping in water. Their seven injured absentees were added to, a couple of hours before kick-off, when Bruno Soriano reported sick. However Juan Carlos Garrido's side went about their business with vim and vigour.

Hernàn Peréz thumped in an early shot which Joe Hart dealt with ably. Then a searching 60-metre pass from Jonathan de Guzmàn gave competition debutant Joselu the flicker of a chance to threaten Hart's goal but the 20-year-old was found wanting.

Sadly, the troubled build-up caught up with them as Villarreal fell behind in the 30th minute. David Silva's pass was perfectly timed to expose the fact that Gonzalo had lost Touré on the edge of the area. The midfielder feinted one way then bent a right-footed shot comfortably beyond Diego López.

The goal reflected the elegance of City's play – they held over 60% of possession at the time – but Garrido will have noted both how hard his patched-up team worked and the degree to which that was appreciated by the El Madrigal faithful.

Effort brought scant reward, however. A half-time rest was beckoning but Balotelli, lively all night, slipped the ball between the legs of José Catalá, sprinted into the box and was tripped, inadvertently, by Mateo Musacchi. Balotelli, growing by the game under Roberto Mancini's tutelage, easily tricked López with the spot kick.

Set against a raucous backdrop of vociferous travelling support and determined replies from the Villarreal faithful it was a night for Silva to show all his skills. He ceaselessly darted into dangerous positions until a leg injury forced his 65th-minute replacement by Adam Johnson.

But if Villarreal felt that the threat was diminished they were wrong. A smart move involving Samir Nasri, Balotelli and Touré five minutes later ended with the Ivorian midfielder dancing past Catalá and burying his second goal. On to Naples for impressive City.

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